Msx1 (msh homeobox 1) - Rat Genome Database

Name: Msx1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Msx1 (msh homeobox 1) Rattus norvegicus

Analyze

Symbol:

Msx1

Name:

msh homeobox 1

RGD ID:

620929

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; p53 binding activity; and transcription cis-regulatory region binding activity. Involved in cartilage development; cellular response to nicotine; and pituitary gland development. Predicted to be located in nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Biomarker of cryptorchidism. Human ortholog(s) of this gene implicated in cleft lip; cleft palate; orofacial cleft 5; tooth and nail syndrome; and tooth disease (multiple). Orthologous to human MSX1 (msh homeobox 1); INTERACTS WITH (S)-nicotine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine; 6-propyl-2-thiouracil.

Type:

protein-coding (Ensembl: pseudogene)

RefSeq Status:

VALIDATED

Previously known as:

homeo box, msh-like 1; homeobox protein MSX-1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	MSX1 (msh homeobox 1)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Msx1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Msx1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	MSX1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	MSX1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Msx1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	MSX1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	MSX1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Msx1 (msh homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	MSX1 (msh homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Msx1 (msh homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	msx1a (muscle segment homeobox 1a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Dr	Alliance	DIOPT (Hieranoid\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	vab-15	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

NCBI Annotation Information:

Annotation category: suggests misassembly; Annotation category: partial on reference assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	14	72,961,170 - 72,964,970 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	72,961,148 - 72,964,966 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	77,415,192 - 77,419,125 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	14	78,656,060 - 78,659,993 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	14	75,096,617 - 75,100,553 (+)	NCBI	Rnor_WKY
Rnor_6.0	14	77,712,262 - 77,716,061 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	77,712,240 - 77,716,059 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	77,690,990 - 77,694,789 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	78,257,345 - 78,261,144 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	78,259,735 - 78,263,533 (+)	NCBI
Celera	14	71,923,586 - 71,927,385 (+)	NCBI		Celera
Cytogenetic Map	14	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

anodontia (ISO)

cleft lip (ISO)

cleft palate (ISO)

Craniofacial Abnormalities (ISO)

Craniosynostosis Syndrome, Autosomal Recessive (ISO)

cryptorchidism (IEP)

Ellis-Van Creveld syndrome (ISO)

Femoral Fractures (IEP)

nonsyndromic deafness (ISO)

orofacial cleft (ISS)

orofacial cleft 5 (ISO)

Selective Tooth Agenesis 1 (ISO)

Stomach Neoplasms (ISO)

Tooth Abnormalities (ISO)

tooth agenesis (ISO,ISS)

tooth and nail syndrome (ISO)

Wolf-Hirschhorn syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(S)-nicotine (EXP)

1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine (EXP)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

4,4'-sulfonyldiphenol (ISO)

5-aza-2'-deoxycytidine (ISO)

6-propyl-2-thiouracil (EXP)

acrylamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenite(3-) (ISO)

belinostat (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cannabidiol (ISO)

carbamazepine (ISO)

choline (ISO)

copper atom (EXP)

copper(0) (EXP)

copper(II) sulfate (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

cyproconazole (ISO)

cytarabine (ISO)

DDT (EXP)

dimethylarsinous acid (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

entinostat (ISO)

flavonoids (EXP)

folic acid (ISO)

formaldehyde (ISO)

furan (EXP)

glycidol (EXP)

hexaconazole (ISO)

L-methionine (ISO)

Licochalcone B (ISO)

mercury dibromide (ISO)

nicotine (EXP)

ozone (ISO)

p-chloromercuribenzoic acid (ISO)

panobinostat (ISO)

paracetamol (ISO)

phenobarbital (ISO)

phenylmercury acetate (ISO)

quercetin (EXP,ISO)

retinyl acetate (ISO)

SB 431542 (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sulindac sulfide (ISO)

temozolomide (ISO)

thioacetamide (EXP)

tributylstannane (ISO)

trichostatin A (ISO)

trimellitic anhydride (ISO)

troglitazone (ISO)

urethane (ISO)

valproic acid (ISO)

vorinostat (ISO)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of meiosis (ISO)

anterior/posterior pattern specification (ISO)

BMP signaling pathway (ISO)

BMP signaling pathway involved in heart development (ISO)

bone morphogenesis (ISO)

cartilage development (IMP)

cartilage morphogenesis (ISO)

cell morphogenesis (ISO)

cellular response to nicotine (IEP)

embryonic digit morphogenesis (ISO)

embryonic forelimb morphogenesis (ISO)

embryonic hindlimb morphogenesis (ISO)

embryonic limb morphogenesis (ISO)

embryonic nail plate morphogenesis (ISO)

epithelial to mesenchymal transition (ISO)

epithelial to mesenchymal transition involved in endocardial cushion formation (ISO)

face morphogenesis (ISO)

forebrain development (ISO)

heart development (ISO)

heart morphogenesis (ISO)

in utero embryonic development (ISO)

mammary gland epithelium development (ISO)

mesenchymal cell apoptotic process (ISO)

mesenchymal cell proliferation (ISO)

midbrain development (ISO)

middle ear morphogenesis (ISO)

muscle organ development (ISO)

negative regulation of apoptotic process (ISO)

negative regulation of cell growth (ISO)

negative regulation of cell population proliferation (ISO)

negative regulation of DNA binding (ISO)

negative regulation of DNA-templated transcription (ISO)

negative regulation of striated muscle cell differentiation (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

negative regulation of transcription regulatory region DNA binding (ISO)

odontogenesis (ISO)

odontogenesis of dentin-containing tooth (ISO)

pituitary gland development (IEP)

positive regulation of BMP signaling pathway (ISO)

positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (ISO)

positive regulation of mesenchymal cell apoptotic process (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

protein localization to nucleus (ISO)

protein stabilization (ISO)

regulation of odontogenesis (ISO)

roof of mouth development (ISO)

signal transduction involved in regulation of gene expression (ISO)

stem cell differentiation (ISO)

transcription by RNA polymerase II (ISO)

Cellular Component

cellular_component (ND)

nucleoplasm (ISO)

nucleus (ISO)

transcription regulator complex (ISO)

Molecular Function

cis-regulatory region sequence-specific DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (ISO)

DNA-binding transcription repressor activity, RNA polymerase II-specific (ISO)

molecular_function (ND)

p53 binding (ISO)

protein binding (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Altered expression of muscle- and cytoskeleton-related genes in a rat strain with inherited cryptorchidism.	Barthold JS, etal., J Androl. 2008 May-Jun;29(3):352-66. Epub 2008 Jan 24.
2.	Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals.	Blin-Wakkach C, etal., Proc Natl Acad Sci U S A 2001 Jun 19;98(13):7336-41.
3.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	[Molecular cloning, expression of rat Msx-1 and Msx-2 during early embryo genesis and roles for mandibular chondrogenesis]	Ishiguro S Kokubyo Gakkai Zasshi. 1999 Mar;66(1):33-45.
6.	Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate.	Jezewski PA, etal., J Med Genet. 2003 Jun;40(6):399-407.
7.	Regulation of MT melatonin receptor expression in the foetal rat pituitary.	Johnston JD, etal., J Neuroendocrinol. 2006 Jan;18(1):50-6.
8.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
9.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
10.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
11.	GOA pipeline	RGD automated data pipeline
12.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
14.	Comprehensive gene review and curation	RGD comprehensive gene curation
15.	A human MSX1 homeodomain missense mutation causes selective tooth agenesis.	Vastardis H, etal., Nat Genet. 1996 Aug;13(4):417-21.
16.	Nicotine promotes cardiomyocyte apoptosis via oxidative stress and altered apoptosis-related gene expression.	Zhou X, etal., Cardiology. 2010;115(4):243-50. Epub 2010 Mar 26.

Additional References at PubMed

PMID:7916326	PMID:8858134	PMID:8861098	PMID:8898217	PMID:9369446	PMID:9697309	PMID:10340755	PMID:10742093	PMID:10742104	PMID:11023873	PMID:11332647	PMID:11369996
PMID:12489152	PMID:12651933	PMID:15188430	PMID:15192231	PMID:15217086	PMID:15705871	PMID:15930102	PMID:16002402	PMID:16330189	PMID:17030628	PMID:17601530	PMID:17693062
PMID:18285513	PMID:18590716	PMID:18667074	PMID:19422820	PMID:20004191	PMID:20123092	PMID:21465616	PMID:22071108	PMID:27741242

Genomics

Comparative Map Data

Msx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	14	72,961,170 - 72,964,970 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	72,961,148 - 72,964,966 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	77,415,192 - 77,419,125 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	14	78,656,060 - 78,659,993 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	14	75,096,617 - 75,100,553 (+)	NCBI	Rnor_WKY
Rnor_6.0	14	77,712,262 - 77,716,061 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	77,712,240 - 77,716,059 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	77,690,990 - 77,694,789 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	78,257,345 - 78,261,144 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	78,259,735 - 78,263,533 (+)	NCBI
Celera	14	71,923,586 - 71,927,385 (+)	NCBI		Celera
Cytogenetic Map	14	q21	NCBI

MSX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	4,859,665 - 4,863,936 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	4	4,859,665 - 4,863,936 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	4,861,392 - 4,865,663 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	4,912,293 - 4,916,564 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	4,979,477 - 4,983,530	NCBI
Celera	4	4,758,413 - 4,762,671 (+)	NCBI		Celera
Cytogenetic Map	4	p16.2	NCBI
HuRef	4	4,797,648 - 4,801,917 (+)	NCBI		HuRef
CHM1_1	4	4,859,330 - 4,863,591 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	4	4,829,290 - 4,833,545 (+)	NCBI		T2T-CHM13v2.0

Msx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	37,977,835 - 37,981,929 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	37,977,829 - 37,981,927 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	37,820,491 - 37,824,585 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	37,820,485 - 37,824,583 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	38,211,730 - 38,215,824 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	38,108,742 - 38,112,705 (-)	NCBI		MGSCv36	mm8
Celera	5	35,276,257 - 35,280,351 (-)	NCBI		Celera
Cytogenetic Map	5	B3	NCBI
cM Map	5	20.21	NCBI

Msx1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955514	4,923,552 - 4,927,471 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955514	4,923,552 - 4,927,471 (-)	NCBI	ChiLan1.0	ChiLan1.0

MSX1
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	4	4,935,603 - 4,939,117 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	4,935,600 - 4,939,079 (+)	Ensembl	panpan1.1		panPan2

MSX1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	3	70,232,790 - 70,236,295 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	3	70,232,052 - 70,236,447 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	3	72,783,942 - 72,787,987 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	3	70,991,546 - 70,995,590 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	3	70,991,361 - 70,995,465 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	3	70,263,330 - 70,267,578 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	3	70,426,128 - 70,430,168 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	3	70,808,811 - 70,812,856 (+)	NCBI		UU_Cfam_GSD_1.0

Msx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405285	63,704,859 - 63,711,968 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936477	17,409,191 - 17,412,919 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936477	17,406,551 - 17,413,615 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

MSX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	5,628,380 - 5,632,607 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	5,628,381 - 5,632,375 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	5,246,698 - 5,250,692 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

MSX1
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	27	41,028,763 - 41,032,676 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	27	41,028,919 - 41,033,006 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666047	87,832,093 - 87,836,013 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Msx1
(Heterocephalus glaber - naked mole-rat)

Naked Mole-rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624755	21,857,461 - 21,861,337 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624755	21,857,360 - 21,861,235 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Msx1
24 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	384
Count of miRNA genes:	212
Interacting mature miRNAs:	248
Transcripts:	ENSRNOT00000009101
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631839	Niddm37	Non-insulin dependent diabetes mellitus QTL 37	3.37		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	11030622	95876975	Rat
70187	Pancm5	Pancreatic morphology QTL 5	16.7		pancreas mass (VT:0010144)	pancreas weight to body weight ratio (CMO:0000630)	14	30320092	80829842	Rat
2313048	Bss84	Bone structure and strength QTL 84	3.1	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	14	37669719	82669719	Rat
2313084	Bss83	Bone structure and strength QTL 83	2.9	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	14	37669719	82669719	Rat
2313089	Bss81	Bone structure and strength QTL 81	3.4	0.0001	body length (VT:0001256)	body length, nose to rump (CMO:0000079)	14	37669719	82669719	Rat
2313100	Bss82	Bone structure and strength QTL 82	3	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	14	37669719	82669719	Rat
738037	Hcas6	Hepatocarcinoma susceptibility QTL 6	2.93		liver integrity trait (VT:0010547)	liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)	14	39057237	83368335	Rat
70214	Niddm28	Non-insulin dependent diabetes mellitus QTL 28	4.06		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	39998251	75582726	Rat
631523	Pia13	Pristane induced arthritis QTL 13	3.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	40793460	98037301	Rat
1300136	Rf22	Renal function QTL 22	3.9		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	14	42262529	95023211	Rat
1549834	Scl45	Serum cholesterol level QTL 45	5.8		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	14	50023211	95023211	Rat
2300197	Scl59	Serum cholesterol level QTL 59			blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	14	55147478	100147478	Rat
9590294	Uminl4	Urine mineral level QTL 4	5.66	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	14	55624247	100624247	Rat
9589034	Epfw11	Epididymal fat weight QTL 11	6	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	14	55624247	100624247	Rat
2317879	Alcrsp27	Alcohol response QTL 27	3.3	0.63	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	14	56631369	101631369	Rat
634328	Hc5	Hypercalciuria QTL 5	2.3		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	14	58184885	103184885	Rat
70153	Bp59	Blood pressure QTL 59	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	14	68757796	83368335	Rat
1582259	Gluco23	Glucose level QTL 23	3.1	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	70053989	104886043	Rat
1641900	Alcrsp11	Alcohol response QTL 11			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	14	70053989	104886043	Rat

Markers in Region

RH130342

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	72,964,607 - 72,964,791 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	77,715,700 - 77,715,883	NCBI	Rnor6.0
Rnor_5.0	14	77,694,428 - 77,694,611	UniSTS	Rnor5.0
RGSC_v3.4	14	78,260,783 - 78,260,966	UniSTS	RGSC3.4
Celera	14	71,927,024 - 71,927,207	UniSTS
Cytogenetic Map	14	q21	UniSTS

AI324650

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	72,964,681 - 72,964,798 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	77,715,774 - 77,715,890	NCBI	Rnor6.0
Rnor_5.0	14	77,694,502 - 77,694,618	UniSTS	Rnor5.0
RGSC_v3.4	14	78,260,857 - 78,260,973	UniSTS	RGSC3.4
Celera	14	71,927,098 - 71,927,214	UniSTS
Cytogenetic Map	14	q21	UniSTS

Msx1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	72,961,262 - 72,961,723 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	77,712,356 - 77,712,815	NCBI	Rnor6.0
Rnor_5.0	14	77,691,084 - 77,691,543	UniSTS	Rnor5.0
Celera	14	71,923,680 - 71,924,139	UniSTS
Cytogenetic Map	14	q21	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium		2							23		9
Low		41	9	4	9	4	8	11	51	23	24	11	8
Below cutoff	3		33	22	10	22				12	8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031059	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF390077	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	D83036	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000254	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000009101 ⟹ ENSRNOP00000009101

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	14	77,712,240 - 77,716,059 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000109302

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	72,961,148 - 72,964,966 (+)	Ensembl

RefSeq Acc Id:

NM_031059 ⟹ NP_112321

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	14	72,961,170 - 72,964,970 (+)	NCBI
Rnor_6.0	14	77,712,262 - 77,716,061 (+)	NCBI
Rnor_5.0	14	77,690,990 - 77,694,789 (+)	NCBI
RGSC_v3.4	14	78,257,345 - 78,261,144 (+)	RGD
Celera	14	71,923,586 - 71,927,385 (+)	RGD

Sequence:

show sequence

GGAACCCAGGAGCTCGCAGAAGCCGGTCAGGAGCTCGCAGAAGCCGGTCGCGCTCCCAGCCTGC
CCGAAACCCATGACCCAGGGCTGTCCCGAGCGCCGTCTGAAGTGGGGGTCCGGCTCTGCAGGGC
CCCGGCTGCTGCTATGACTTCTTTGCCACTCGGTGTCAAAGTGGAGGACTCCGCCTTCGCCAAG
CCTGCTGGGGGAGGCGCTGCCCAGGCCCCCGGGGCTGCTGCGGCCACTGCAACCGCCATGGGCA
CAGATGAGGAGGGCGCCAAGCCCAAAGTGCCCGCTTCACTCCTGCCCTTCAGCGTGGAGGCCCT
CATGGCCGATCACAGGAAGCCCGGGGCAAAGGAGAGCGTCCTGGTGGCTTCCGAAGGGGCTCAG
GCGGCGGGTGGCTCGGTGCAGCACTTGGGCACCCGGCCCGGGTCTCTGGGCGCCCCGGACGCGC
CCTCCTCGCCGGGGCCTCTCGGCCATTTCTCTGTTGGGGGACTCCTCAAGCTGCCAGAAGATGC
TCTGGTGAAGGCCGAGAGCCCGGAGAAGCTAGATCGGACCCCGTGGATGCAGAGTCCCCGCTTC
TCCCCGCCCCCAGCCAGGCGGCTGAGTCCCCCGGCCTGCACCCTACGCAAGCACAAGACCAACC
GCAAGCCCAGGACGCCCTTCACCACGGCTCAGCTACTGGCTCTGGAGCGCAAGTTCCGCCAGAA
GCAGTACCTGTCTATTGCCGAGCGCGCCGAGTTCTCCAGCTCGCTCAGCCTTACCGAGACCCAG
GTGAAGATCTGGTTCCAGAACCGCCGTGCTAAGGCCAAGAGACTGCAGGAGGCCGAGTTGGAGA
AGTTGAAGATGGCCGCGAAGCCAATGTTGCCGCCTGCTGCGTTCGGCCTCTCCTTTCCTCTTGG
GGGTCCTGCAGCGGTGGCTGCAGCTGCCGGCGCCTCACTCTACAGTGCCTCTGGCCCTTTCCAG
CGCGCCGCGCTGCCTGTAGCGCCCGTGGGACTCTACACCGCCCACGTAGGCTACAGCATGTACC
ACCTGACATAGGTGGGCCCAGAGTCACCTCCCTGTGGTGCCATCCCTTCCCCAGCCACCTCTTC
TAGGCAGCGGGAGTCCTTCCTAGGAAGCTCTGCTGCCCAACACCACCTGGCCCCTTCTCTTAAA
CCCTTCGCTACACAGTTCCTCCTGGCCATCGCATCTTAAAATTCCTCCTCCCTCTTCCGACCCC
TTCTGGGAAGAAAAAAAAGTGGCCGGAAGTGTCTAGGTTTTTCGAGAAAAATTTATATTTACAC
GTGCGAGTTATAAATGTGGAAACTGGGGGATGCAAAGGCGAAGAGATTTATCCGTGGTCCCCAG
CAGAATTAAAGGCTGAAGGAGACCAGAGGCCAAAAGGACTAGAGGCCATGAGACTCCATCAGCT
GCTTCCGGTCCTGAAACCAGGCAGGACTGCACAGAGAAATTGTTATTTGGTGCTCCAAGAGACG
AGCCCAGCCCTATAGAAAGCAAGGAGCACAGCTCCTTCCATTGTCAGACTCCAAACGCATTGCA
GCAAAGCATTGCTCTGAGGGGGCAGGGTGCATGCTGCTGGTTCACGAAGGTAGGTTGAAGAGAC
TTTCCCAGGACCAGAAAAAAAGAAGTTAAAAAACAAAATCTGTTTCTATTTAACAGTACATTTT
CGTGGCTCTCAAACATCCCTTTTGAAGGGATCGTGTGTACTATGTAATATACTGTATATTTGAA
ATTTTATTATCATTTATATTATAGCTATATTTGTTAAATAAATTAATTTTAAGCTACAAAAAAA
AAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_112321	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK70504	(Get FASTA)	NCBI Sequence Viewer
	BAA11750	(Get FASTA)	NCBI Sequence Viewer
	EDM00020	(Get FASTA)	NCBI Sequence Viewer
	EDM00021	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_112321 ⟸ NM_031059

- Sequence:

show sequence

MTSLPLGVKVEDSAFAKPAGGGAAQAPGAAAATATAMGTDEEGAKPKVPASLLPFSVEALMADH
RKPGAKESVLVASEGAQAAGGSVQHLGTRPGSLGAPDAPSSPGPLGHFSVGGLLKLPEDALVKA
ESPEKLDRTPWMQSPRFSPPPARRLSPPACTLRKHKTNRKPRTPFTTAQLLALERKFRQKQYLS
IAERAEFSSSLSLTETQVKIWFQNRRAKAKRLQEAELEKLKMAAKPMLPPAAFGLSFPLGGPAA
VAAAAGASLYSASGPFQRAALPVAPVGLYTAHVGYSMYHLT

hide sequence

RefSeq Acc Id:

ENSRNOP00000009101 ⟸ ENSRNOT00000009101

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V6U7-F1-model_v2	AlphaFold	G3V6U7	1-297	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620929	AgrOrtholog
BioCyc Gene	G2FUF-15370	BioCyc
Ensembl Genes	ENSRNOG00000006876	Ensembl
	ENSRNOG00000068566	Ensembl
InterPro	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
KEGG Report	rno:81710	UniProtKB/TrEMBL
NCBI Gene	81710	ENTREZGENE
Pfam	Homeobox	UniProtKB/TrEMBL
PhenoGen	Msx1	PhenoGen
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	Q9QUG0_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-09	Msx1	msh homeobox 1	Msx1	homeo box, msh-like 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Msx1	homeo box, msh-like 1			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Msx1	homeo box, msh-like 1			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in dental and craniofacial tissues	724434

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

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